//============================================================================
// Name        : Lab.cpp
// Author      : Anthea Neums, Jonas Halbach
//			   :
// Description : Uses the PatternGenomAnalyser to match Genoms and Patterns.
//============================================================================

#include <iostream>
#include <fstream>
#include <string>
#include "FileReader/FileReader.h"
#include "PatternAnalyser/PatternHandler.h"
#include "PatternAnalyser/PatternGenomAnalyser.h"
#include "PatternAnalyser/Found.h"
#include "tests/Test.h"

#include <list>

#define TEST

using namespace std;

#ifdef RELEASE

int main() {

	cout << "Test begin:" << endl;

	testFileLoading();
	testPatternMatching();

	showTestGenom();


	cout << "Test end!" << endl;
	return 0;
}



#else

int main() {
	//FileReader *contentReader = new FileReader((char *)"txt/testfiles/testpattern.txt");
	//char *testPattern = (char *)"txt/testfiles/testpattern.txt";
	//char *testGenom = (char *)"txt/testfiles/testgenom.txt";
	char *testPattern = (char *)"txt/GenomPattern3.txt";
    char *testGenom = (char *)"txt/GenomProbe.txt";
	//char *testPattern = (char *)"txt/testfiles/Pattern_short.txt";
	//char *testGenom = (char *)"txt/testfiles/GenomProbe_short.txt";

	//char *testPattern = (char *)"txt/testfiles/leerPattern.txt";
	//char *testGenom = (char *)"txt/testfiles/LeerGenom.txt";

	//char *testPattern = (char *)"txt/testfiles/A_Pattern.txt";
	//char *testGenom = (char *)"txt/testfiles/A_Genom.txt";
	//FileReader *reader = new FileReader(testPattern);
	//cout << "getContent"<<reader->getContent() << endl;

	algorithm::PatternGenomAnalyser *patternGenomAnalyser = new algorithm::PatternGenomAnalyser(testPattern, testGenom);

	patternGenomAnalyser->findSimilarStrings();

	patternGenomAnalyser->printFounds();



	return 0;
}

#endif
